This question is based on http://stackoverflow.com/questions/359424/detach-subdirectory-into-separate-git-repository Instead of detaching a single subdirectory, I want to detach a couple. For example, my current directory tree looks like this: /apps /AAA /BBB /CCC /libs /XXX /YYY /ZZZ And I would like this instead: /apps /AAA /libs /XXX The --subdirectory-filter argument to git filter-branch won't work because it gets rid of everything except for the given directory the first time it's run. I thought using the --index-filter argument for all unwanted files would work (albeit tedious), but if I try running it more than once, I get the following message: Cannot create a new backup. A previous backup already exists in refs/original/ Force overwriting the backup with -f Any ideas? TIA